braney: changes by file

review to branch (2009-09-22 to 2009-09-29) v216

• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.17 lines changed: 17, context: html, text, full: html, text
    add bounds output
  • 1.16 lines changed: 1, context: html, text, full: html, text
    oops, default should be to use 32 bits
  • 1.15 lines changed: 122, context: html, text, full: html, text
    added -bed12, -max, and -zero options. Made default counting unit size and unsigned long
• src/hg/bedSplitOnChrom/bedSplitOnChrom.c
  • 1.3 lines changed: 14, context: html, text, full: html, text
    add a little optimization to avoid hash search on each line
  • 1.2 lines changed: 25, context: html, text, full: html, text
    added a couple of options to facilitate use in ENCODE pipeline
• src/hg/encode/converters/pairedTagToBed12/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a program to convert a pairedTag file into a bed12 with a couple of sequences
• src/hg/encode/converters/pairedTagToBed12/pairedTagToBed12.c
  • 1.1 lines changed: 83, context: html, text, full: html, text
    a program to convert a pairedTag file into a bed12 with a couple of sequences
• src/hg/encode/converters/tagToBed12/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a program to convert a tagAlign file into a bed12 with a couple of sequences
• src/hg/encode/converters/tagToBed12/tagToBed12.c
  • 1.1 lines changed: 82, context: html, text, full: html, text
    a program to convert a tagAlign file into a bed12 with a couple of sequences
• src/hg/hgTracks/simpleTracks.c
  • 1.105 lines changed: 1, context: html, text, full: html, text
    make barb colors be the same color as the line and box.
• src/hg/inc/bed12wSeq.h
  • 1.1 lines changed: 96, context: html, text, full: html, text
    a header file for bed12 plus a pair of sequences
• src/hg/lib/bed12wSeq.as
  • 1.1 lines changed: 18, context: html, text, full: html, text
    bed12 plus a couple of sequences at the end
• src/hg/lib/bed12wSeq.c
  • 1.1 lines changed: 294, context: html, text, full: html, text
    bed12 plus a couple of sequences at the end
• src/hg/lib/bed12wSeq.sql
  • 1.1 lines changed: 24, context: html, text, full: html, text
    bed12 plus a couple of sequences at the end
• src/hg/lib/makefile
  • 1.397 lines changed: 2, context: html, text, full: html, text
    add a few files to the library (yay! it's even bigger now ;-)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.544 lines changed: 181, context: html, text, full: html, text
    add LogSignal tracks for Hannon lab
  • 1.541 lines changed: 18, context: html, text, full: html, text
    reload wiggles for Hannon lab
  • 1.537 lines changed: 159, context: html, text, full: html, text
    Hannon lab short rna edits
  • 1.535 lines changed: 22, context: html, text, full: html, text
    shortened and editing some labels for Affy/CSHL exons
  • 1.534 lines changed: 342, context: html, text, full: html, text
    new Hannon lab short RNA data
  • 1.532 lines changed: 849, context: html, text, full: html, text
    drop all the old Hannon lab stuff so I can start over
  • 1.530 lines changed: 1, context: html, text, full: html, text
    move Gis Pet to variation